[English] 日本語
Yorodumi
- PDB-8tcb: Structure of human C4b-binding protein alpha chain CCP domains 1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tcb
TitleStructure of human C4b-binding protein alpha chain CCP domains 1 and 2 in complex with the hypervariable region of group A Streptococcus M87 protein
Components
  • C4b-binding protein alpha chain
  • M protein
KeywordsIMMUNE SYSTEM / immune evasion / human complement
Function / homology
Function and homology information


regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / RNA binding ...regulation of opsonization / response to symbiotic bacterium / negative regulation of complement activation, classical pathway / T cell mediated immunity / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of protein catabolic process / blood microparticle / innate immune response / RNA binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / : / Streptococcal M proteins C repeat profile. / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...C4b-binding protein alpha, oligomerization domain / Oligomerization domain of C4b-binding protein alpha / M protein repeat / M protein repeat / : / Streptococcal M proteins C repeat profile. / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
: / C4b-binding protein alpha chain / M protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsMcGowan, M.A. / Kolesinski, P. / Ghosh, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI154149 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Conservation of C4BP-binding sequence patterns in Streptococcus pyogenes M and Enn proteins.
Authors: Kolesinski, P. / McGowan, M. / Botteaux, A. / Smeesters, P.R. / Ghosh, P.
History
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C4b-binding protein alpha chain
C: M protein
D: M protein
B: C4b-binding protein alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4305
Polymers53,3914
Non-polymers391
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.176, 73.802, 190.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein C4b-binding protein alpha chain / C4bp / Proline-rich protein / PRP


Mass: 14163.894 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C4BPA, C4BP / Production host: Escherichia coli (E. coli) / References: UniProt: P04003
#2: Protein M protein


Mass: 12531.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: emm / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TLP8
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, pH 4.8, 0.2 M KH2PO4, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→68.81 Å / Num. obs: 17478 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 54.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 20.3
Reflection shellResolution: 2.69→2.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2045 / CC1/2: 0.452 / Rpim(I) all: 0.641 / Rrim(I) all: 1.155 / % possible all: 90.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→68.81 Å / SU ML: 0.4636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2784 872 5.01 %
Rwork0.2353 16542 -
obs0.2375 17414 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.45 Å2
Refinement stepCycle: LAST / Resolution: 2.69→68.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 1 29 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372732
X-RAY DIFFRACTIONf_angle_d0.61863740
X-RAY DIFFRACTIONf_chiral_restr0.0327430
X-RAY DIFFRACTIONf_plane_restr0.0038490
X-RAY DIFFRACTIONf_dihedral_angle_d4.1576392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.860.37431330.3492521X-RAY DIFFRACTION92.09
2.86-3.080.36211450.28372754X-RAY DIFFRACTION99.97
3.08-3.390.26851430.24732718X-RAY DIFFRACTION99.97
3.39-3.880.28311470.22342789X-RAY DIFFRACTION100
3.88-4.890.22811470.19052805X-RAY DIFFRACTION99.97
4.89-68.810.28581570.24272955X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.846591113163.157819801114.762922622583.13867756414.738180668495.154020180530.280891960766-0.229334518224-0.2489754405270.5056022561710.0102436295481-0.05185147912920.334909975474-0.190130704653-0.3564378517820.420038721242-0.0612807006263-0.06151047477660.399792590740.07195476745040.487962809828-10.70392416670.36158191822-38.0491643541
22.60676622596-0.5364999851923.723775190250.102116200926-1.266472272225.07282828889-0.3029588176190.1530812741310.1479595835760.12625379627-0.1847794144840.0551472133731-0.4372281919850.4003259977510.3993815766570.7049808002940.06648140982950.003228689103960.282819660692-0.003703343086040.4103484495370.503482321591-11.3269047356-44.3105631161
30.6962197347420.6291949497721.917370115191.541953152012.863026926446.75779643488-0.0234889057609-0.104701978442-0.08307969798830.3115950173-0.1952435623880.4331016137050.444346547953-0.3566118247080.3286564470810.4455309384280.03901543050270.09845415852250.347645802681-0.01351791988540.453659324930.719618590383-13.7748618772-34.0822505348
41.79045166064-0.473864664833-0.4281154420853.277270583620.01385969446166.33886151846-0.361343406510.00907325550642-0.149295390150.7830504284890.01810155439890.06513055496220.4486932555820.01282121417180.2977060162720.486758918217-0.005926254953110.01015209115550.213372941321-0.02463232151930.438886990759.73423316505-24.636288152-42.3971113476
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 0 through 124)AA0 - 1241 - 122
22(chain 'C' and resid 46 through 125)CB46 - 1251 - 80
33(chain 'D' and resid 46 through 110)DC46 - 1101 - 65
44(chain 'B' and resid 1 through 122)AA00D1 - 1221 - 112

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more